DGKB
Basic information
Region (hg38): 7:14145049-14974777
Previous symbols: [ "DAGK2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKB gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 23 | 23 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 23 | 0 | 0 |
Variants in DGKB
This is a list of pathogenic ClinVar variants found in the DGKB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-14149208-T-C | not specified | Uncertain significance (Apr 22, 2022) | ||
7-14149217-G-T | not specified | Uncertain significance (Mar 18, 2024) | ||
7-14176894-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
7-14178047-A-C | not specified | Uncertain significance (Jun 22, 2023) | ||
7-14338538-T-C | not specified | Uncertain significance (Dec 22, 2023) | ||
7-14574296-C-A | not specified | Uncertain significance (Oct 26, 2021) | ||
7-14574332-A-C | not specified | Uncertain significance (Nov 29, 2023) | ||
7-14580883-T-C | not specified | Uncertain significance (Sep 28, 2022) | ||
7-14580939-A-G | not specified | Uncertain significance (Mar 26, 2024) | ||
7-14583134-T-A | not specified | Uncertain significance (May 30, 2024) | ||
7-14607486-G-C | not specified | Uncertain significance (Aug 17, 2022) | ||
7-14621393-A-T | not specified | Uncertain significance (Apr 15, 2024) | ||
7-14621413-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
7-14621428-T-C | not specified | Uncertain significance (Oct 17, 2023) | ||
7-14682641-T-A | Uncertain significance (Feb 08, 2023) | |||
7-14682763-C-T | not specified | Likely benign (May 13, 2024) | ||
7-14694114-C-T | not specified | Uncertain significance (Mar 12, 2024) | ||
7-14698108-G-C | not specified | Uncertain significance (Feb 05, 2024) | ||
7-14701685-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
7-14718628-G-A | not specified | Uncertain significance (Oct 17, 2023) | ||
7-14718646-G-A | not specified | Uncertain significance (Mar 16, 2022) | ||
7-14718649-C-T | not specified | Uncertain significance (May 04, 2022) | ||
7-14718665-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
7-14718679-C-A | not specified | Uncertain significance (Dec 09, 2023) | ||
7-14736053-G-C | not specified | Uncertain significance (Aug 13, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DGKB | protein_coding | protein_coding | ENST00000403951 | 25 | 829729 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.530 | 0.470 | 125009 | 0 | 11 | 125020 | 0.0000440 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.95 | 296 | 406 | 0.728 | 0.0000207 | 5259 |
Missense in Polyphen | 64 | 147.24 | 0.43466 | 1916 | ||
Synonymous | -0.824 | 150 | 138 | 1.09 | 0.00000716 | 1419 |
Loss of Function | 4.92 | 10 | 46.0 | 0.218 | 0.00000235 | 590 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000896 | 0.0000896 |
Ashkenazi Jewish | 0.0000995 | 0.0000993 |
East Asian | 0.0000552 | 0.0000550 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000357 | 0.0000353 |
Middle Eastern | 0.0000552 | 0.0000550 |
South Asian | 0.0000656 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Exhibits high phosphorylation activity for long-chain diacylglycerols. {ECO:0000250}.;
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Effects of PIP2 hydrolysis;Platelet activation, signaling and aggregation;Glycerophospholipid metabolism;Hemostasis;G alpha (q) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- rvis_EVS
- -0.93
- rvis_percentile_EVS
- 9.61
Haploinsufficiency Scores
- pHI
- 0.178
- hipred
- Y
- hipred_score
- 0.601
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.958
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dgkb
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- protein kinase C-activating G protein-coupled receptor signaling pathway;response to bacterium;platelet activation;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;modulation of chemical synaptic transmission;regulation of postsynapse organization
- Cellular component
- cytoplasm;plasma membrane;Schaffer collateral - CA1 synapse;glutamatergic synapse
- Molecular function
- NAD+ kinase activity;diacylglycerol kinase activity;calcium ion binding;ATP binding